7 files changed, 56 insertions, 12 deletions

diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
index fe7a6db..1aa748a 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala
@@ -59,6 +59,7 @@ object RSAComb extends App {
       )
 
     val answers = rsa ask queries
+    Logger print s"Number of answers: ${answers.length}"
 
     /* Write answers to output file */
     os.write(
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
index 2b165c4..a0d567e 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala
@@ -214,7 +214,7 @@ class RSAOntology(
   /** Retrieve individuals/literals in the ontology */
   private val individuals: List[IRI] =
     ontology
-      .getIndividualsInSignature()
+      .getIndividualsInSignature(Imports.INCLUDED)
       .asScala
       .map(_.getIRI)
       .map(implicits.RDFox.owlapiToRdfoxIri)
@@ -588,23 +588,44 @@ class RSAOntology(
     RDFoxUtil.addData(data, RSAOntology.CanonGraph, datafiles: _*)
 
     /* Top/equality axiomatization */
+    RDFoxUtil.updateData(data, 
+      s"""
+      INSERT { 
+        GRAPH ${RSAOntology.CanonGraph} { ?X a ${IRI.THING} }
+      } WHERE {
+        GRAPH ${RSAOntology.CanonGraph} { ?X ?Y ?Z }
+      }
+      """
+    )
+    RDFoxUtil.updateData(data, 
+      s"""
+      INSERT { 
+        GRAPH ${RSAOntology.CanonGraph} { ?Z a ${RSA.NAMED} }
+      } WHERE {
+        GRAPH ${RSAOntology.CanonGraph} { ?X ?Y ?Z }.
+        FILTER( ?Y != a )
+      }
+      """
+    )
     RDFoxUtil.addRules(data, topAxioms ++ equalityAxioms)
     Logger.write(topAxioms.mkString("\n"), "axiomatisation.dlog")
     Logger.write(equalityAxioms.mkString("\n"), "axiomatisation.dlog")
 
     /* Introduce `rsacomb:Named` concept */
-    data.evaluateUpdate(
-      null, // the base IRI for the query (if null, a default is used)
-      RSA.Prefixes,
+    /* From data */
+    RDFoxUtil.updateData(data, 
       s"""
       INSERT { 
         GRAPH ${RSAOntology.CanonGraph} { ?X a ${RSA.NAMED} }
       } WHERE {
         GRAPH ${RSAOntology.CanonGraph} { ?X a ${IRI.THING} }
       }
-      """,
-      new java.util.HashMap[String, String]
+      """
     )
+    /* From ontology */
+    val named = individuals.map(RSA.Named(RSAOntology.CanonGraph)(_))
+    RDFoxUtil.addFacts(data, RSAOntology.CanonGraph, named)
+    Logger.write(named.mkString("", ".\n", ".\n"), "canonical_model.dlog")
 
     /* Add canonical model */
     Logger print s"Canonical model facts: ${this.canonicalModel.facts.length}"
@@ -630,7 +651,7 @@ class RSAOntology(
       RDFoxUtil.addRules(data, filter.rules)
 
       // TODO: We remove the rules, should we drop the tuple table as well?
-      data.clearRulesAxiomsExplicateFacts()
+      //data.clearRulesAxiomsExplicateFacts()
 
       /* Gather answers to the query */
       val answers = RDFoxUtil
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxConverter.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxConverter.scala
index 505937b..d9f000d 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxConverter.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/converter/RDFoxConverter.scala
@@ -350,7 +350,7 @@ trait RDFoxConverter {
         (List(atom), List())
       }
 
-      /** Existential class expression (for data properties).
+      /** Existential class expression (for object properties).
         *
         * Parameter `skolem` is used to determine the skolemization
         * technique (if any) to use for the translation.
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/DataFactory.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/DataFactory.scala
index 848c6b5..863122e 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/DataFactory.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/DataFactory.scala
@@ -25,5 +25,5 @@ class DataFactory(private var counter: Integer) {
     Variable.create(f"I${this.getNext()}%05d")
 
   def getOWLClass(): OWLClass =
-    DataFactory.factory.getOWLClass(s"X${this.getNext()}")
+    DataFactory.factory.getOWLClass(RSA(s"tmp${this.getNext()}").getIRI)
 }
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/Logger.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/Logger.scala
index 0fcde53..f3b0232 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/Logger.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/Logger.scala
@@ -112,6 +112,8 @@ echo "\n[Import data]"
             .map(d => s"""import > rsacomb:CanonicalModel \"$d\"""")
             .mkString("\n")
           ++ s"""
+insert { graph rsacomb:CanonicalModel { ?x a owl:Thing } } where { graph rsacomb:CanonicalModel { ?x ?y ?z } }
+insert { graph rsacomb:CanonicalModel { ?z a owl:Thing } } where { graph rsacomb:CanonicalModel { ?x ?y ?z } . filter( ?y != a ) }
 import "axiomatisation.dlog"
 insert { graph rsacomb:CanonicalModel { ?x a rsacomb:Named } } where { graph rsacomb:CanonicalModel { ?x a owl:Thing } }
 
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
index e3e7dd4..d4e55d8 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RDFoxUtil.scala
@@ -183,7 +183,7 @@ object RDFoxUtil {
   /** Imports a sequence of files directly into a datastore.
     *
     * @param data datastore connection.
-    * @param graph named graph where the data should be uploaded
+    * @param graph named graph where the data should be uploaded.
     * @param files sequence of files to upload.
     */
   def addData(data: DataStoreConnection, graph: IRI, files: os.Path*): Unit =
@@ -200,6 +200,23 @@ object RDFoxUtil {
       Logger.DEBUG
     )
 
+  /** Execute an update SPARQL query on a datastore.
+    *
+    * @param data datastore connection.
+    * @param query update SPARQL query.
+    */
+  def updateData(data: DataStoreConnection, query: String): Unit =
+    Logger.timed(
+      data.evaluateUpdate(
+        null, // the base IRI for the query (if null, a default is used)
+        RSA.Prefixes,
+        query,
+        new java.util.HashMap[String, String]
+      ),
+      "Updating data",
+      Logger.DEBUG
+    )
+
   /** Force materialization in RDFox. */
   def materialize(data: DataStoreConnection): Unit =
     Logger.timed(data.updateMaterialization(), "Materialization", Logger.DEBUG)
diff --git a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala
index 5abb83c..6ea4dc6 100644
--- a/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala
+++ b/src/main/scala/uk/ac/ox/cs/rsacomb/util/RSA.scala
@@ -47,9 +47,12 @@ object RSA {
 
   /** Set of default prefixes to be included in all datastore operations */
   val Prefixes: Prefixes = new Prefixes()
-  Prefixes.declarePrefix("rsacomb:", "http://www.cs.ox.ac.uk/isg/RSAComb#")
-  Prefixes.declarePrefix("rdfox:", "http://oxfordsemantic.tech/RDFox#")
+  Prefixes.declarePrefix("xml:", "http://www.w3.org/XML/1998/namespace")
+  Prefixes.declarePrefix("rdf:", "http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+  Prefixes.declarePrefix("rdfs:", "http://www.w3.org/2000/01/rdf-schema#")
   Prefixes.declarePrefix("owl:", "http://www.w3.org/2002/07/owl#")
+  Prefixes.declarePrefix("rdfox:", "http://oxfordsemantic.tech/RDFox#")
+  Prefixes.declarePrefix("rsacomb:", "http://www.cs.ox.ac.uk/isg/RSAComb#")
 
   /** Creates a `rsacomb:<name>` IRI */
   def apply(name: Any): IRI =